[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?
jalemkul at vt.edu
Sat May 21 00:13:46 CEST 2016
On 5/20/16 5:54 PM, Christopher Neale wrote:
> Dear Users:
> I find that gmx make_ndx will create groups with names that have ampersands in them and that this complicates piping the group name back into an analysis tool. I have included an example below. There is an obvious solution with sed to rename the group in the .ndx file after creation (this is what I am doing now). However, I'm thinking about posting a redmine feature request since ideally I think the tool will not require an external step for name-based selection and I wanted to ask here first just in case I am missing something.
Groups can be renamed within make_ndx itself. This does require you to know the
group numbers ("name X mygroup", if you know X), but it's what I usually use
since the number of default groups is predictable.
> ### commands
> echo "aC316 C216"
> echo "aC316 C216 & r1-64"
> echo "aC316 C216 & r65-128"
> echo q
> } | gmx make_ndx -f start.gro -o rdf.ndx
> echo -e 'C316_C216_&_r_65-128\nC316_C216_&_r_65-128\n' | gmx rdf -f MD.xtc -n rdf.ndx -s MD.tpr
> ### output from gmx rdf:
> :-) GROMACS - gmx rdf, VERSION 5.1.2 (-:
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
> GROMACS: gmx rdf, VERSION 5.1.2
> Executable: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
> Data prefix: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
> Command line:
> gmx rdf -f MD.xtc -n rdf.ndx -s MD.tpr
> Program: gmx rdf, VERSION 5.1.2
> Error in user input:
> Invalid selection 'C316_C216_&_r_65-128 '
> Near '&'
> syntax error
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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